my $self = shift;

    my $target = $self->target();
    my $source = $self->source();
    my $dbh    = $self->dbh();
    $self->debug("Vega danio specific - copying internal clone names to seq_region_attrib");

#get id for 'fpc_clone_id' attribute

    $dbh->do("INSERT INTO $target.attrib_type (code,name,description)".
            "values ('fpc_clone_id','fpc clone','clone id used for linking to Zebrafish webFPC')");

    my ($attrib_id) = $dbh->selectrow_array("Select attrib_type_id from $target.attrib_type where code = 'fpc_clone_id'");
    warn "No attrib id found\n" unless defined($attrib_id);

#get clone details
    my $select1_sth = $dbh->prepare
        ("SELECT seq_region_id, name from $target.seq_region where coord_system_id = 3;");
    $select1_sth->execute();
    my ($seq_region_id, $embl_name);
    $select1_sth->bind_columns(\$seq_region_id,\$ embl_name);

    my $clone_name;
    my $select2_sth = $dbh->prepare("select name from $source.clone where embl_acc= ?");

    my $insert_sth = $dbh->prepare("insert into $target.seq_region_attrib values (?,$attrib_id,?)");

    while ($select1_sth->fetch()) {
        $embl_name =~ s/([\d\w]+).*/$1/;
        $select2_sth->bind_param(1,$embl_name);
        $select2_sth->execute;
        $insert_sth->bind_param(1,$seq_region_id);
        while (my ($clone_name) = $select2_sth->fetchrow_array()) {
            $insert_sth->bind_param(2,$clone_name);
            $insert_sth->execute();
        }
    }

    my $self = shift;
    my $target_cs_name = shift;

    my $target = $self->target();
    my $source = $self->source();
    my $dbh    = $self->dbh();

    # clone_info, current_clone_info
    $self->debug("Vega Danio_specific - Transforming clone_id into seq_region_id for clone_info and current_clone_info");

    foreach my $table_name ('clone_info','current_clone_info') {
        my $select_st1 = 
            "SELECT ctg.name, ctg.clone_id " .
            "FROM   $source.contig ctg, $source.$table_name ci " .
            "WHERE  ctg.clone_id = ci.clone_id " .
            "AND ctg.name not like 'ctg%' " .
            "AND ctg.name not like 'NA%'";

        my $query_results1 = $dbh->selectall_arrayref($select_st1);

        my $i = 0;
        foreach my $contig_name (@$query_results1) {
            my $embl_acc = $contig_name->[0];
            my $select_st2 = 
                "SELECT sr.seq_region_id " .
                "FROM $target.seq_region sr " . 
                "WHERE sr.name = '$embl_acc'";
            my @query_results2 = $dbh->selectrow_array($select_st2);
            push @{$query_results1->[$i]},@query_results2;
            $i++;
        }

        foreach my $clone (@$query_results1) {
            my $seq_reg_id = $clone->[2];
            my $clone_id = $clone->[1];

            my $update_query = 
                "UPDATE $target.$table_name " .
                "SET clone_id = '$seq_reg_id' " .
                "WHERE clone_id = '$clone_id'";
            $dbh->do($update_query);
        }
        my $alter_struct_1 = 
            "ALTER table $target.$table_name " .
            "CHANGE clone_id seq_region_id int(10) not null";
        my $alter_struct_2 = 
            "ALTER table $target.$table_name " .
            "add unique index (seq_region_id)";
        $dbh->do($alter_struct_1);
        $dbh->do($alter_struct_2);
    }

    # assembly_tag
    $self->debug("Vega Danio_specific - Transforming contig_id into seq_region_id for assembly_tag");

    # first remove orphans from assembly_tag table (i.e. entries pointing to 
    # non-existing contigs)
    my $numrows = $dbh->do(qq(
        DELETE at
        FROM $source.assembly_tag at
        LEFT JOIN $source.contig c ON c.contig_id = at.contig_id
        WHERE c.contig_id IS NULL
    ));
    $self->debug("  Deleted $numrows orphans from assembly_tag");

    my $select_st3 = 
        "SELECT ctg.name, ctg.contig_id " .
        "FROM   $source.contig ctg, $source.assembly_tag at " .
        "WHERE  ctg.contig_id = at.contig_id " .
        "AND ctg.name not like 'ctg%' " .
        "AND ctg.name not like 'NA%'";

    my $query_results3 = $dbh->selectall_arrayref($select_st3);

    my $j = 0;
    foreach my $contig_name (@$query_results3) {
        my $embl_acc = $contig_name->[0];
        my $select_st4 = 
            "SELECT sr.seq_region_id " .
            "FROM $target.seq_region sr " . 
            "WHERE sr.name = '$embl_acc'";
        my @query_results4 = $dbh->selectrow_array($select_st4);
        push @{$query_results3->[$j]}, @query_results4;
        $j++;
    }

    foreach my $contig (@$query_results3) {
        my $seq_reg_id = $contig->[2];
        my $contig_id = $contig->[1];

        my $update_query = 
            "UPDATE $target.assembly_tag " .
            "SET contig_id = '$seq_reg_id' " .
            "WHERE contig_id = '$contig_id'";
        $dbh->do($update_query);
    }

    $dbh->do("  ALTER TABLE $target.assembly_tag
                CHANGE contig_id seq_region_id int(10) UNSIGNED NOT NULL");

    $dbh->do("  ALTER TABLE $target.assembly_tag
                CHANGE contig_start seq_region_start int(10)");

    $dbh->do("  ALTER TABLE $target.assembly_tag
                CHANGE contig_end seq_region_end int(10)");

    $dbh->do("  ALTER TABLE $target.assembly_tag
                CHANGE contig_strand seq_region_strand tinyint(1)");

}

1;